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- PDB-1ee1: CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS ... -

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Entry
Database: PDB / ID: 1ee1
TitleCRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH ONE MOLECULE ATP, TWO MOLECULES DEAMIDO-NAD+ AND ONE MG2+ ION
ComponentsNH(3)-DEPENDENT NAD(+) SYNTHETASE
KeywordsLIGASE / LYASE / AMIDOTRANSFERASE / NH3 DEPENDENT / ATP PYROPHOSPHATASE
Function / homologyNAD(+) synthetase / Rossmann-like alpha/beta/alpha sandwich fold / NAD/GMP synthase / NH(3)-dependent NAD(+) synthetase / NAD synthase / NAD+ synthase / NAD+ synthase (glutamine-hydrolyzing) activity / NAD+ synthase activity / NAD biosynthetic process / sporulation resulting in formation of a cellular spore ...NAD(+) synthetase / Rossmann-like alpha/beta/alpha sandwich fold / NAD/GMP synthase / NH(3)-dependent NAD(+) synthetase / NAD synthase / NAD+ synthase / NAD+ synthase (glutamine-hydrolyzing) activity / NAD+ synthase activity / NAD biosynthetic process / sporulation resulting in formation of a cellular spore / ATP binding / metal ion binding / cytoplasm / NH(3)-dependent NAD(+) synthetase
Function and homology information
Specimen sourceBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / 2.06 Å resolution
AuthorsDevedjiev, Y. / Symersky, J. / Singh, R. / Jedrzejas, M. / Brouillette, C. / Brouillette, W. / Muccio, D. / Chattopadhyay, D. / Delucas, L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis.
Authors: Devedjiev, Y. / Symersky, J. / Singh, R. / Jedrzejas, M. / Brouillette, C. / Brouillette, W. / Muccio, D. / Chattopadhyay, D. / DeLucas, L.
#1: Journal: AM.CRYST.ASSOC.,ABSTR.PAPERS (SUMMER MEETING) / Year: 1997
Title: Asymmetric Complex of NAD+ Synthetase with Natural Substrates ATP Deamido-NAD+
Authors: Devedjiev, Y. / Singh, R. / Brouillette, C. / Muccio, D. / Brouillette, W. / DeLucas, L. / Jedzejas, M.
#2: Journal: AM.CRYST.ASSOC.,ABSTR.PAPERS (SUMMER MEETING) / Year: 1998
Title: Catalytic Cycle of NAD+ Synthetase Viewed by X-Ray Structures of Kinetic Intermediates
Authors: Devedjiev, Y. / Singh, R. / Brouillette, C. / Muccio, D. / Brouillette, W. / DeLucas, L. / Jedzejas, M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 28, 2000 / Release: Jun 6, 2001
RevisionDateData content typeGroupCategoryProviderType
1.0Jun 6, 2001Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Oct 4, 2017Structure modelRefinement descriptionsoftware

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: NH(3)-DEPENDENT NAD(+) SYNTHETASE
B: NH(3)-DEPENDENT NAD(+) SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4706
Polyers60,6082
Non-polymers1,8624
Water7,152397
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8560
ΔGint (kcal/M)-63
Surface area (Å2)20670
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)52.98, 86.69, 60.48
Angle α, β, γ (deg.)90.0, 111.18, 90.0
Int Tables number4
Space group name H-MP 1 21 1

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Components

#1: Protein/peptide NH(3)-DEPENDENT NAD(+) SYNTHETASE / NAD(+) SYNTHETASE


Mass: 30303.994 Da / Num. of mol.: 2 / Source: (gene. exp.) Bacillus subtilis (bacteria) / Genus: Bacillus / Gene: NADEGrenade / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli)
References: UniProt: P08164, NAD+ synthase (glutamine-hydrolysing)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Chemical ChemComp-DND / NICOTINIC ACID ADENINE DINUCLEOTIDE / DEAMIDO-NAD+


Mass: 665.418 Da / Num. of mol.: 2 / Formula: C21H27N6O15P2
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 / Density percent sol: 42.42 %
Crystal growTemp: 298 K / Method: vapor diffusion / pH: 5.2
Details: PEG400, sodium acetate, magnesium chloride, adenosine triphosphate, deamido-NAD+, pH 5.2, VAPOR DIFFUSION, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
120 mMsodium acetate1drop
250 mM1dropMgCl2
32.5 mMbeta-mercaptoethanol1drop
415 mg/mlprotein1drop
521-23 %(v/v)PEG4001reservoir
60.1 Msodium acetate1reservoir
750 mM1reservoirMgCl2
85 mMNaAD1reservoir
90.5 mMATP1reservoir

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Data collection

DiffractionMean temperature: 298 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Collection date: Mar 20, 1997
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 25.3 Å2 / D resolution high: 2.06 Å / D resolution low: 2 Å / Number all: 98810 / Number obs: 33464 / Observed criterion sigma F: 1 / Observed criterion sigma I: 1 / Rmerge I obs: 0.05 / NetI over sigmaI: 13.3 / Redundancy: 2.9 % / Percent possible obs: 95.6
Reflection shellRmerge I obs: 0.156 / Highest resolution: 2.06 Å / Lowest resolution: 2.13 Å / Number unique all: 2584 / Redundancy: 2.5 % / Percent possible all: 82.6
Reflection
*PLUS
Number obs: 30068 / Number measured all: 136657 / Percent possible obs: 95.4 / Rmerge I obs: 0.05
Reflection shell
*PLUS
Percent possible obs: 83 / MeanI over sigI obs: 7.8

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Processing

Software
NameClassification
X-PLORrefinement
SCALEPACKdata scaling
RefineDetails: Used weighted least squares procedure. ALL PORTIONS OF THE BACKBONE IN SUBUNIT A ARE WELL ORDERED. HOWEVER, BACKBONE ATOMS AND THE SIDE CHAINS OF RESIDUES 83-86 AND 205-225 IN SUBUNIT B ARE NOT VISIBLE ON THE ELECTRON DENSITY MAP. THE NICOTINIC ACID MOIETY OF DEAMIDO-NAD BOUND TO SUBUNIT B IS DISORDERED AS WELL, THOUGH THE REMAINDER OF THE SUBSTRATE IS WELL ORDERED. COORDINATES OF THE NICOTINIC ACID MOIETY IN SUBUNIT B ARE PRESENTED FOR REFERENCE. ATP BINDING SITE IN SUBUNIT A IS FULLY OCCUPIED, HOWEVER, NO BINDING OF ATP AND MG2+ WAS FOUND IN SUBUNIT B.
R Free selection details: RANDOM / Sigma F: 1 / Sigma I: 1 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.219 / R factor R work: 0.154 / R factor all: 0.154 / R factor obs: 0.154 / Highest resolution: 2.06 Å / Lowest resolution: 6 Å / Number reflection R free: 1240 / Number reflection all: 28724 / Number reflection obs: 23848 / Percent reflection obs: 95
Refine hist #LASTHighest resolution: 2.06 Å / Lowest resolution: 6 Å
Number of atoms included #LASTProtein: 4068 / Nucleic acid: 0 / Ligand: 120 / Solvent: 397 / Total: 4585
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.010
X-RAY DIFFRACTIONx_angle_deg2.07
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine
*PLUS
Sigma F: 1
Least-squares process
*PLUS
R factor obs: 0.158 / Lowest resolution: 6 Å / Number reflection obs: 29684
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg2.2

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